R Notebook

require(scales)

Loading required package: scales

Attaching package: ‘scales’

The following object is masked from ‘package:readr’:

    col_factor

Calculate averages for clusters from resolution 1.5:

v2 <- VlnPlot(seurobj, features.plot='percent.mito', point.size.use=-1, group.by='res.1.5', y.max=0.2)
v2

#Average expression is calculated by: (mean(1expm(seurobj@data[gene, cluster])))
#average.expression <- AverageExpression(SetAllIdent(seurobj, id='res.1.5'))

BATLAS results.

batlas <- read.table('../tables/tables_paper/supplementary_tables/BATLAS/BATLAS.txt', header=T, sep='\t')
batlas$cluster <- as.character(batlas$cluster)
kable(batlas)

|cluster | brown| white|
|:-------|-----:|-----:|
|0       | 0.389| 0.611|
|1       | 0.471| 0.529|
|2       | 0.384| 0.616|
|3       | 0.600| 0.400|
|4       | 0.567| 0.433|
|5       | 0.422| 0.578|
|6       | 0.315| 0.685|
|7       | 0.607| 0.393|
|8       | 0.560| 0.440|
|9       | 0.680| 0.320|
|10      | 0.479| 0.521|
|11      | 0.545| 0.455|
|12      | 0.420| 0.580|
|13      | 0.542| 0.458|
|14      | 0.723| 0.277|
|15      | 0.443| 0.557|
|16      | 0.845| 0.155|
|17      | 0.769| 0.231|
|18      | 0.488| 0.512|
|19      | 0.446| 0.554|
|20      | 0.390| 0.610|
|21      | 0.578| 0.422|

BATLAS results log normalized.

batlas <- read.table('../tables/tables_paper/supplementary_tables/BATLAS/BATLAS_log_normalized.txt', header=T, sep='\t')
batlas$cluster <- as.character(batlas$cluster)
kable(batlas)

|cluster | brown| white|
|:-------|-----:|-----:|
|0       | 0.569| 0.431|
|1       | 0.590| 0.410|
|2       | 0.564| 0.436|
|3       | 0.634| 0.366|
|4       | 0.618| 0.382|
|5       | 0.578| 0.422|
|6       | 0.539| 0.461|
|7       | 0.635| 0.365|
|8       | 0.623| 0.377|
|9       | 0.659| 0.341|
|10      | 0.594| 0.406|
|11      | 0.618| 0.382|
|12      | 0.579| 0.421|
|13      | 0.618| 0.382|
|14      | 0.677| 0.323|
|15      | 0.579| 0.421|
|16      | 0.730| 0.270|
|17      | 0.697| 0.303|
|18      | 0.595| 0.405|
|19      | 0.583| 0.417|
|20      | 0.526| 0.474|
|21      | 0.634| 0.366|

p <- ggplot(data=batlas, aes(x=cluster, y=brown)) +
  geom_bar(stat="identity") +
  ylab('Brown percentage estimate') +
  coord_flip()
p